Well, I have a German Shepard and he does fine with cats and he wasn't introduced to them until he was almost 2.
If you get a puppy, I agree it should be fine. Puppies are generally easier to acclimate to strange things. Not always though. You could also try to find a breeder who has cats!
I don't know much about Doberman's, but I do know they are very smart. I also know, like any breed you have to be VERY selective on where you get the puppy. Irresponsible breeders can lead you down a path of nothing but heartache. CTChin is the doberman expert, and i'm sure she'll give her 2 cents on it. If nothing else, you can pm her for her input.
German Shepards are wonderful dogs. BUT.... they are high maintenance. Shepards require a lot of brushing, and they need a good amount of activity. Shepards are smart, loyal, and protective.
If I had to pick, I'd pick a shepard but that's only because I don't know enough about Doberman's to bring that breed into my home at this time. Before buying any breed I suggest research, research, research....
Both breeds have genetic defects that parents should be tested for. All in all, its a tough choice. Good luck.